Genetics of one-carbon metabolism in sheep in relation to productivity, fertility and health

该项目的重点是羊的健康、生产力和福利。我们将专注于影响终身健康和福祉的代谢方面。具体来说，我们将研究代谢的一个关键方面，称为一碳（1C）代谢。这很重要，因为它影响细胞中的许多关键过程，包括DNA合成，DNA甲基化和细胞增殖。它通过传递甲基来做到这一点，甲基是这些生化反应的核心。参与这些途径的代谢物，如胆碱、蛋氨酸、叶酸和维生素B12的缺乏，对动物的发育和健康有不利影响。例如，维生素B12和/或叶酸的缺乏会影响生育力和胎儿发育，并导致成年动物和人类的生长不良、血管疾病和代谢综合征。1C代谢途径复杂，受多种基因的影响。我们假设这些基因的突变会影响1C代谢和动物对微量营养素缺乏的脆弱性。在这项研究中，我们将确定这样的突变，确定其功能意义，（即它们的作用和重要性），测试它们对不同饮食的动物的影响，并找到利用这些信息改善农场动物福利的方法。在直接影响1C代谢的大约40个基因中，以及在参与能量代谢、细胞增殖、DNA合成和DNA甲基化。为了在绵羊中实现这一点，我们将创建自己的序列数据。我们估计，我们将确定2000-4000 SNPs通过这些方法。然后，我们会进行一项大规模的研究，从本地屠宰场屠宰的约300只绵羊中收集肝脏样本。我们将对每个样本进行基因分型（以确定存在哪些SNP），测量基因表达并对参与1C代谢的所有代谢物进行全面分析。对这些数据的解释将使我们了解SNP的功能以及这些SNP如何影响1C代谢途径。为了实现这一目标，我们将整理所需的信息，并利用我们对这些基因组的了解结合复杂的生物信息学分析，确定对1C代谢影响最大的SNP子集。我们希望在这些基因中鉴定出大约100个功能显著的SNP。然后，我们将构建一个“SNP芯片”，即一种同时对绵羊进行基因分型的工具。该芯片将用于筛选几群绵羊，以识别24只“低风险”和24只“高风险”断奶羔羊，以及24只“低风险”和24只“高风险”繁殖母羊。然后，我们将在涉及对照和甲基缺乏饮食（即两种基因型两种饮食）的单独研究中监测这些动物。对于断奶羔羊，我们将重点关注对生长、动物健康和肝脏代谢以及胴体产量和组成的影响。对于繁殖母羊，我们还将关注动物健康和肝脏代谢，但扩展研究以考虑对早期（第16天）雄性和雌性胚胎中DNA化学修饰（即DNA甲基化）的影响。这项研究将为1C代谢的许多组分的营养x基因相互作用以及它们如何影响（a）羔羊生产效率，健康和福利，以及（B）哺乳动物胚胎的早期发育影响生育力和后代的长期健康和福祉提供新的见解。我们将能够利用这些信息来帮助培育具有更好功能的1C代谢的动物（导致福利和生产力的永久改善）和/或改善动物饮食。由于1C代谢也影响人类的发育和健康，我们的研究结果也将具有生物医学研究的益处，并增加绵羊作为这种研究模式物种的实用性。

This project is focussed on the health, productivity and welfare of sheep. We will concentrate on aspects of metabolism that affect lifelong health and wellbeing. Specifically, we will study a key aspect of metabolism referred to as one-carbon (1C) metabolism. This is important because it affects many key processes in the cell, including DNA synthesis, DNA methylation and cell proliferation. It does this by delivering methyl groups, which are central to these biochemical reactions. Deficiencies in metabolites involved in these pathways, such as choline, methionine, folate and vitamin B12, have adverse effects on animal development and wellbeing. For example, deficiencies in vitamin B12 and/or folate can affect fertility and fetal development, and lead to poor growth, vascular disease and metabolic syndrome in adult animals and humans. 1C metabolism pathways are complex and are affected by many genes. We hypothesise that mutations in these genes will affect 1C metabolism and the vulnerability of animals to micronutrient deficiencies. In this study we will identify such mutations, determine their functional significance (i.e. what they do and how important they are), test their impact in animals fed different diets, and find ways to use this information to improve the welfare of farm animals.Firstly, we will identify mutations (i.e. single nucleotide polymorphisms or SNPs) in around 40 genes directly affecting 1C metabolism, and in very closely related pathways involved in energy metabolism, cell proliferation, DNA synthesis and DNA methylation. To achieve this in sheep we will create our own sequence data. We estimate that we will identify 2000-4000 SNPs by these methods. We will then conduct a large-scale study with liver samples collected from around 300 sheep slaughtered at local abattoirs. We will genotype each sample (to determine which SNPs are present), measure gene expression and conduct a comprehensive analysis of all metabolites involved in 1C metabolism. Interpretation of these data will inform us on SNP function and how these SNPs affect pathways involved in 1C metabolism. To achieve this we will collate the required information and, using our knowledge of these genomes combined with complex bioinformatic analyses, determine the subset of SNPs that have the greatest impact on 1C metabolism. We expect to identify an estimated 100 or so functionally significant SNPs in these genes. We will then construct a 'SNP chip'; i.e. a tool to genotype sheep simultaneously and cheaply for many SNPs. This chip will be used to screen several flocks of sheep to identify 24 'Low-risk' and 24 'High-risk' weaned lambs, and 24 'Low-risk' and 24 'High-risk' breeding ewes. We will then monitor these animals in separate studies involving Control and Methyl-Deficient diets (i.e. two genotypes by two diets). For weaned lambs we will focus on effects on growth, animal health and liver metabolism, and carcass yields and composition. For breeding ewes we will also focus on animal health and liver metabolism, but extend studies to consider effects on chemical modifications to DNA (i.e. DNA methylation) in early (Day 16) male and female embryos. This research will provide novel insights into nutrient x gene interactions for many components of 1C metabolism and how they affect (a) lamb production efficiency, health and welfare, and (b) early development of mammalian embryos influencing fertility and the long-term health and wellbeing of offspring. We will be able to use this information to help breed animals with better functioning 1C metabolism (leading to permanent improvements in welfare and productivity) and/or to improve animal diets. As 1C metabolism also influences human development and health our results will also have biomedical research benefits, and increase the utility of sheep as a model species for this type of research.